From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Nov 30 2007 - 10:05:43 CST
Dear Jerome,
You mentioned in this reply to Luca that you could point him to few
papers that describe how to derive the gradient of a reaction
coordinated depending on several distances in Cartesian coordinates.
Could you write me the citations of these paper(s)?
Thanks a lot
vlad
Jerome Henin wrote:
>Hi Luca,
>
>On Nov 30, 2007 4:22 AM, luca <bellucci14_at_unisi.it> wrote:
>
>
>>On Friday 30 November 2007 00:37:54 you wrote:
>>Hi Jerome,
>>Thank for replay.
>>
>>
>>>Dear Luca,
>>>If your "more advanced reaction coordinate" is a single variable that
>>>depends on several distances, you just have to work out a few
>>>equations (mostly the gradient of that variable in Cartesian
>>>coordinates). I can point you to a few papers if you need it.
>>>
>>>
>>I am interested on this argument. I have been reading some article this week , but
>>I think that this is a difficult work to implement ...in fast and easy way.
>>
>>
>
>That is true. Implementing new coordinates takes some time and effort,
>except in the simplest cases. That is why we encourage people who
>write them to contribute them so that others in the community do not
>duplicate the work.
>
>
>
>>>If what you really want is to define a multidimensional free energy
>>>surface, function of several distances, then the NAMD ABF code cannot
>>>currently do that.
>>>
>>>
>>Yes, I'm sorry I had this in mind .
>>
>>
>>>We are working on making this possible in future
>>>versions, but there is no release schedule yet.
>>>
>>>
>>Ok. I will see http://www.edam.uhp-nancy.fr/ABF/index.html
>>At this moment I can run multiple md with different reaction coordinates and
>>make FES manually. Do You have a reference/suggestion for this approach?
>>
>>
>
>I can see two cases:
>1) The different coordinates are not significantly correlated. In this
>case, the free energy will be additive:
>A(x1, x2, x3) = A1(x1) + A2(x2) + A3(x3)
>and all the information is contained in the 1-D profiles.
>
>2) The coordinates are correlated. That can still be treated if you
>can define discrete states for most of the coordinates, e.g. if the
>1-D profiles have a small number of free energy basins. Then you could
>compute 1-D PMFs with all other coordinates restrained to a specific
>state, and repeat this procedure for all states you consider
>interesting.
>Of course, this only works if you have a good intuitive understanding
>of the system already, and it gets impractical if there are many
>coordinates/states, but it may help get "semi-quantitative" results.
>
>Jerome
>
>
>
>
-- ---------------------------------------------------------------------------- Dr. Vlad Cojocaru EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Tel: ++49-6221-533266 Fax: ++49-6221-533298 e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------
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